Naruto: retaliation
by scouttroop
Summary: This a sequel to Naruto rise of cobra. The Konoha shinobi alliance will face Cobra commander again but they will also be on the run from a crime they didn't commit. It's time for retaliation.
1. Marking territory

**Marking territory**

**Hey everyone here's Naruto: retaliation the sequel of Naruto: rise of cobra.**

**Disclaimers: I don't own Naruto or GI Joe, Masashi Kishimoto and Hasbro own them.**

Bandit hideout

"Hassle up you guys find the hostage and get her out of there", Ino said to the trio who are heading for the gate.

Sasuke, Kakashi and Shikamaru got to the gate.

"Hey Choji are ready with that 18 year old aim?" Kakashi said while he puts on his heat gloves to make an opening.

"Yes I am Kakashi sensei", Choji said.

Kakashi then burns the gate and made an opening and the trio heads in.

"Alright Choji were in give us that diversion", Kakashi ordered Choji.

"I'm on it", Choji throws a high power senbon needle breaking a coffee cup that one bandit was holding.

After the bandits are distracted Sasuke flash a red light hoping to find the hostage he flashed it 6 times until the hostage flashes her red light at a wagon covered by a sheet.

"Alright let's go, Shikamaru you stay put", Sasuke and Kakashi move out but Shikamaru isn't going to stay put.

2 bandits are running but Sasuke and Kakashi attacks them. Sasuke knocks one out after waking the guy in the face and last one gets knocked out after Kakashi smacks him very hard.

"Did I know you fight ugly?" Sasuke said to Kakashi.

"Not from their backs they don't", Kakashi said.

They move to the wagon until Kakashi notice Shikamaru is climbing up the watch tower.

"Shikamaru what the hell are doing?"

"He's making our territory Kakashi sensei", Choji answered.

"Choji if you see Shikamaru you shoot him", Kakashi warn him.

"My pleasure", Choji agreed to Kakashi.

Sasuke and Kakashi remove the sheet from the wagon and the girl climbs out. Sasuke and Kakashi grab the girl and move back to the opening.

"Shikamaru get your ass back to the team", Ino said in the radio but he's not answering.

"I don't see him do you see him?" Ino asked Choji because she can't even see him even with her binoculars.

"Oh you're not going to believe this Kakashi sensei", Choji said after spotting something very interesting.

Kakashi looks to the right and sees the shinobi alliance flag.

**END of chapter**

**Prologue**

The 4th shinobi war rages on and Sasuke Uchiha now leads his own team of the shinobi alliance. Under Sasuke's command are Kakashi Hatake, Ino Yamanaka, Shikamaru Nara and Yugao Uzuki.

The ruthless terrorist known as Cobra commander and Destro have been capture by the shinobi alliance and place in a maximum security prison, but the cobra operatives Storm shadow and Kabuto Yakushi remain at large.

The shinobi alliance and the entire elemental nation remain on high alert for all of Cobra commander's final vow.

Retaliation

**Ok that's the first chapter in this new story. I hope you like it. Please review. I just have a question who gets to play General Colton?**

**Next: Mission and set up**


	2. Mission then set up

**Mission then set up**

**Hello everyone I have been busy with GSD terran empire so I come back here for now with the next chapter.**

In the last chapter Sasuke and his team infiltrated a hideout of bandits to rescue a girl and it was a success. While they were doing that Shikamaru place the shinobi alliance flag.

In Konoha Kakashi's house

Sasuke and Kakashi are playing a game.

"I'm bleeding out, I'm right there", Kakashi then stares at Sasuke's character that's spinning.

"Are you spinning? How could you be good in combat if you're spinning?"

After they turn the thing off 2 of Kakashi's daughters climb on Sasuke and played with him. Few years after having Cobra commander and Destro imprisoned Kakashi reunited with Hanare and married her and she gave him 2 daughters. Also they heard that there was assassination attempted on the Mizukage in Kirigakure but the assassination failed.

Elsewhere

The leaders of the elemental nations are discussing their course of action ever since the assassination attempt on the Mizukage. Despite the assassination failed a large scroll was stolen. The fire daimyo arrive tells them about the plan to retrieve the stolen scroll. None are aware that's Kabuto in disguise.

"Get me the Sasuke Uchiha's team", the fire daimyo/Kabuto ordered.

Timeskip

"Alright that scroll could not have gone far once we have it will have it transported back to Kirigakure. Ino and Shikamaru take the lead and Kakashi will give you support."

"Hell yeah", Kakashi said grabbing an m249 lmg.

"Hey Choji in my first drop I pop a live round in mouth get your teeth to chatter give it a shot", Kakashi gives it to Choji and he puts it in his mouth.

"Delicious", Choji said.

"Atta boy", Kakashi said to him after hearing that.

"Ino what are we up against?" Sasuke asked Ino.

"Renegade samurais are armed with swords, bows and arrows."

"Wow what you got there?" Shikamaru asked Ino about her m26 MASS shotgun ammunition.

"P-dub 381 black tempest, fire one of these they are remote control by your weapon", Ino briefs Shikamaru.

"When do we get these?" Shikamaru asked while holding the p-dub.

"We didn't we did", Ino said.

"Let me see", Shikamaru tries to reach for it but Ino says no touch.

"Girls with guns", Choji said before Shikamaru covers the camera screen.

Soon they reached their destination they get ready.

"Kakashi sensei say a few words", Sasuke said to him.

"I mean a few words whatever might guide my life, but if I chow before I wake I accept my fate, hell yeah?"

"Hell yeah!" everyone said it but Sasuke was the loudest.

"Hell yeah", Kakashi ready's his m249 lmg.

"Make way let's go, let's go", Sasuke said to everyone.

"Anyone missing Yugao", Shikamaru asked after noticing Yugao isn't with them.

"I train with Yugao for years if she isn't here she has a good reason", Kakashi said to Shikamaru.

"Weapons check?" Sasuke said to the rest of the team and they all said check.

"As you're good sensei you need new gloves", Kakashi said to Sasuke.

"Hoorah?!" Sasuke said to the others and they said the same.

"Remember use your guns only in an emergency, the enemy are samurais so can take them easily", Sasuke reminded them.

They split into different groups, they watched all the samurais chat before Kakashi and his group hook down and attack them. They use their kunai, shuriken, jutsu, bare hands and their guns but just when they need it, Kakashi use his clock 21 (same one use by Roadblock). Choji spots a samurai coming up behind Sasuke, he fires his m26 MASS and controls the p-dub and kills the samurai.

"I own you one Choji", Sasuke said.

"Clear", Choji before moving on.

Sasuke with Ino then finds the scroll but it's guarded by 2 samurai archers.

"Were pin down needs some assistance", Sasuke shouted and help jump to him and Ino.

"Tango down", one random shinobi alliance member said.

After that Sasuke and Ino grab the scroll and regroup with the others.

"Radio command", Kakashi said.

"I'm on that", a random member said.

"More renegade samurais closing in", one random member on the radio warned them.

"Mount up, let's mount up", Sasuke ordered.

Timeskip

They regroup in a desert base and they got the scroll transported back to Kirigakure.

"Good job Choji", Sasuke said to Choji.

"All that Wii combat shooter finally paying off", Choji said before walking off.

"Ha hah bam!" Shikamaru said in funny way.

Elsewhere

The fire daimyo and his people have been informed that the mission has been a success by Sasuke and they cheered.

Back the desert base shooting raged.

"So let me get this strait, one whole weekend your looking after my little girls and my wife", Kakashi said about Sasuke's weekend while he loads his FN SCAR-H rifle.

"I Love your girls I really do but they lived to terrorise me and so does your wife Hanare", Sasuke said about Kakashi's family.

"And if you win."

"You have to take your next promotion", Sasuke said.

Sasuke then aims his FN SCAR-H rifle at the candle. Kakashi keeps on interrupting Sasuke when he is trying to aim. It was Kakashi turn for a shot but he wins when he uses a browning m2 aircraft hmg. Sasuke said that didn't count but Kakashi doesn't pay attention to him anyway.

Meanwhile

The fire daimyo/Kabuto calls his bodyguards who are actually agents of Cobra to escort him to the bunker where the real fire daimyo is being kept. After getting there he shows him something Kabuto pulls out a kunai knife and scratch his face with it and his faces shift shape into his real face before changing back into the fire daimyo's face again.

"Your insane", the real fire daimyo said after seeing that.

"Well before anything else happens tell me where's the prison location where Cobra commander is being kept", Kabuto asked him.

Back at the desert base

A squadron Uh-60 blackhawk are on their way to the Sasuke's team. The team quickly spots them and then the blackhawks open fires at them. Sasuke and all of them tried to shoot them down with their guns and jutsu but the blackhawks armor is like the cobra gunship.

"Take cover", Sasuke shouted.

Sasuke then saves Shikamaru from being hit but the vehicle behind him explodes and takes Sasuke with it.

"SASUKE!" Shikamaru screamed to him but no reply.

Ino and Kakashi also tried calling Sasuke but no answer, Kakashi ordered all them to jump into the water well. The airstrike is over and 2 cobra troopers armed with m4 assault rifles search for survivors and eliminate them. The cobra troopers open fire inside the water well hoping for movement. When none came they leave the scene not knowing Kakashi, Ino and Shikamaru are still alive.

**End of this chapter, Sasuke is not dead he will appear in the epilogue chapter. The use of guns is only when they need it. The airstrike I use replace the apaches with cobra UH-60 blackhawk helicopters instead. Please review.**

**Next: Cobra commander returns**


	3. Cobra commander returns

**Cobra commander returns**

**Hello again in this chapter get ready for Cobra commander's return. I hope you enjoy this chapter.**

**Disclaimers: I own nothing**

On the last chapter ordered by the fire daimyo, Sasuke and his team were sent to retrieve a stolen scroll right after a failed assassination attempt on the Mizukage. Sasuke and his team were successful on retrieving it and transporting back to Kirikagure. Meanwhile the fire daimyo/Kabuto went to ask the real fire daimyo about the location were Cobra commander is imprisoned. Back at the desert base Sasuke and his team are attacked by a squadron of cobra UH-60 blackhawk helicopters and they killed a lot of the team including Sasuke or sort of. 2 cobra troopers search for any survivors including from a water well when none came they leave the scene.

Sometime later the fire daimyo/Kabuto made an announcement to everyone in the elemental nation about Sasuke and his team's betrayal which turns out to be a lie but not everyone is aware it's a lie, as for the assassination attempt was caused by Yugao Uzuki but it's also a lie. They will be replace by a new Special Forces codename cobra.

Meanwhile back at the ruined desert base

Kakashi, Ino and Shikamaru are climbing their way out of the water well and back to the surface. After they made it back to the surface they find the whole base in ruins.

"Everyone's dead", Shikamaru said sadly.

"Were going find who did this to our brothers and to Sasuke", Kakashi said while place an m4 rifle on the ground making it look like a cross.

Sunagakure maximum security prison

Suna anbu guards bring the prisoner Yugao but they are unaware if that was really Yugao they upper handed.

Timeskip

Matsuri was in charge of the place and introduce the other 2 prisoners, Cobra commander and Destro.

"Welcome to hell", Matsuri said to Yugao.

"You have no idea", Yugao's voice changes to a man's voice and went puff revealing its Storm shadow posing a Yugao.

"Storm shadow so you tried to assassinate the Mizukage", Matsuri said and place both of Storm shadow down on the stairs while the crew puts a white suit on him then in the water tube he goes.

Back at the desert

Shikamaru asked Kakashi about contacting someone for help but he says the cobra UH-60 blackhawks destroyed it.

"What!? How is anyone going to know were still alive", Shikamaru asked Kakashi.

"They won't because where not, to our allies, to our families especially to our enemy we were KIA in this desert."

"We have to at least try there might someone still alive."

"No any record and traces of our existence is terminated the only one I trust out there is Yugao. When we got hit, how we got hit we were set up right from the start."

Shikamaru then ask about who could call an attack like that, Ino said it can't be from a high ranking ninja, it could be from a non-ninja.

"No there's only man who could authorize a strike like that and I voted for him", Kakashi might already know who ordered that.

Back at Suna

Outside the prison a man in his wheel blaster bike stops from a distance from the gate and activates small robotic fireflies and directs to the gate and the guards.

Inside

Storm shadow inside the tubes sees the robot firefly in the security camera and he pretends his heart stopped. When the guards tries to pull him out Storm shadow pulls one into the tube and Matsuri sees what's happening now.

"Oh my kami, stop him", Matsuri order.

Matsuri hides while Storm shadow kills all 3 guards with shurikens even snapping ones neck. Back outside the guards are wondering about the fireflies around them. One lets one firefly on his hand and checks it and then they all detonate killing them all.

Back inside

Storm shadow retrieves both his swords and making it into a staff sword once more and he hides after hearing more guards coming. The guards come into the room then Storm shadow ambush them and cuts them all down.

"Welcome to hell", Storm shadow said to Matsuri with an evil smile on his face.

Matsuri then electrocutes him with those heart pumpers and she runs away from the room.

Outside Firefly drives his bike toward the gate then open fire with the mounted mp7 smgs then fires missile, next he gets off his bike as all the parts turns into missiles too. He parachutes to make his landing safe, now he pulls out his duel pistols and heads inside.

Back inside again

Storm shadow pulls out a hidden revolver and shoots the tube freeing Cobra commander. Cobra commander removes some of the stuff and then puts his mask back on. Matsuri is trying to open gate the leads to the surface but the door is stuck.

"Storm shadow never adapt", Cobra commander said.

"Cobra commander", Storm shadow hands the revolver to him.

Cobra commander then turns to Destro.

"Destro, your out of the band", Cobra commander decides to leave Destro imprisoned.

Matsuri is still trying to get the gate open but the gate automatically opens and a single metal ball rolls next to her. It then detonates and Matsuri falls down on the floor injured and Firefly stands where he is.

"I see you have arranged transportation", Cobra commander said while he and Storm shadow leaves the room and Firefly walks up to them.

"Making things go boom by 9: am which most people do all day."

"Firefly good to see you old friend", Cobra commander greeted him.

"Sir some people didn't want let me in, I busted out 8 prisoners but I only broke into 1. All communication has been cut off no one will know that your even missing."

An injured Matsuri interrupted the conversation by throwing a kunai at a flammable tube but it failed to kill them and Cobra commander shoots her in the stomach knocking her out, Storm shadow manage to reach the elevator but his back was badly burned.

"Take him to the mountains to heal I'll continue the war that's still going on", Cobra commander orders Firefly.

Outside Yugao watches Cobra commander, Storm shadow and Firefly get out with her binoculars. Yugao pulls out her pistol but she too late to stop them as the cobra helicopter flies away with them.

"Well I guess this war won't be over soon with Cobra commander back in action", Yugao said as she heads inside to check for survivors.

Zeus industrial complex unknown location

2 cobra troopers open the double doors for Cobra commander (retaliation suit) and Firefly to come in.

"Sir Launch controls are nearly up the director is running behind", a cobra trooper said.

"I hear his behind no one or anywhere else for that matter", Firefly said.

"Armored prototype completed to your specs. You'll like this working title high speed sentry HISS", a cobra trooper introduce the HISS tank.

"It's good to have you back sir."

Cobra commander and Firefly got into the elevator and sees their new weapon.

"Isn't she a beauty?"

"Soon the elemental nation will cower in the face of Zeus", Cobra commander tells Firefly.

"All we been missing is our commander. Good to have you back boss", Firefly said.

"Cool mask", fire daimyo/Kabuto walked up to them.

"Someone took his time."

"Not easy to be in that bath in a tube."

"Just don't forget who put you there", Cobra commander warns him.

"On the rock you crawled out from", Firefly said.

"Firefly, it's good to know that were still running low on crazy, still hold ten fingers."

Firefly wiggles his fingers and gives Kabuto the middle finger.

"How's our former fire daimyo?"

"He work his way on a platter, you know they call a work to bore but I never get bored."

"In 48 hours Zeus will launch", Cobra commander reminds him.

"Just one wrinkle 3 of Sasuke's team somehow survive that little house cleaning, a drone pick up voices prints in the desert", Kabuto warns him.

"Can I trust you with nothing", Cobra commander talks to him angrily.

"They'll slip up and when they do I'll own the ground", Firefly tells him he will deal with them.

"Hoorah", Cobra commander said.

**END**

**Who gets to play General Colton**

**Next: Arashikage plan and new help**


	4. Author's message

**Author's message**

**To my fellow readers I'm not discontinuing Naruto: retaliation I just need to know a character who can have the role of General Colton, I already have Tsunade playing General Hawk and Shizune as Cover girl in Naruto: rise of cobra. You readers can give me a character on who can have the role. The rest of the chapter leave that to me. **

**After I get my answer on who gets to have General Colton's role I'll do the next chapter.**


	5. Arashikage plan and new help

**Arashikage plan and new help**

**Ok now I have a character to play General Colton so here's the next chapter. I hope you enjoy.**

**Disclaimers: I own nothing**

In the last chapter Kakashi, Ino and Shikamaru left the desert to find who killed their troops and Sasuke with it, during their walk Kakashi says how they got hit is they were set up right from the start but it can't be from any high ranking ninja and Kakashi knows who capable of it. Meanwhile in Sunagakure Storm shadow and Firefly frees Cobra commander but leaves Destro imprisoned. Cobra commander has a new weapon to use against the shinobi alliance, it's a satellite known as Zeus. Kabuto then warns him that Kakashi, Ino and Shikamaru survived the massacre, at first Cobra commander wasn't too happy about the news but Firefly tells him he will handle it.

Arashikage building

"Foes, the massacre in the desert and now Cobra commander and Storm shadow escape prison, it's our time to join the fight and defend the honor of our fellow shinobi alliance", the blind master said.

"Jinx cousin to Storm shadow", the blind master introduce Jinx to Yugao.

In the mountains Storm shadow is strapped to a medical machine were an old women is healing him with powder, black liquid goo and the machine. Storm shadow does feels some pain.

Back at the Arashikage building Yugao and Jinx spare, Jinx is blindfolded but she knows what shes doing. While they were fighting the blind master tells them they must capture Storm shadow because he might know more of Cobra's plans and he fears what happen to the shinobi alliance may only be the beginning. Yugao kicks Jinx making her move back and then she removes her blind folded.

"Enough Yugao I know you doubt Jinx's loyalty but she Arashikage the longer we wait the stronger Storm shadow. You will use this sword to capture Storm shadow so we can bring him to Justice and restore the Arashikage's name."

Yugao sheaths the black Katana and leaves with Jinx.

Elsewhere

Kakashi, Ino and Shikamaru went back to Konoha but they hide in the long abandon Namikaze home. While Kakashi and Shikamaru work Ino tries to contact any surviving member from their team.

Yugao's driving a dune buggy with Jinx sitting next to her spinning a shuriken. Yugao stares at for a moment then she pulls the throttle and drives faster. Ino starts to contact them.

"This isn't restricted to shinobi alliance?"

"There alive", what Jinx said surprise Yugao.

"Ino Yamanaka this is Jinx and Yugao were in pursuit of Storm shadow", Jinx tells Ino in the screen channel.

Back at the Namikaze home

"Well even if Yugao and Jinx grab Storm there still half way around the world were on our own", Kakashi said while pointing his custom glock pistol.

"This is no war, were fighting an army", Shikamaru reminded him.

The conversation is halted when Ino came to show them something about the fire daimyo an image of a few days before then a year later.

"What if the fire daimyo isn't the fire daimyo", Ino said which made them suspect something is not quite right.

"Look if now know the fire daimyo is imposter we could only assume there's no one we can trust", Shikamaru said.

"There is one we can trust and he is the reason why I have the white fang name", Kakashi said to them.

Timeskip

Kakashi began ringing the bell from his old home, well he rang the doorbell 5 times and nobody answer. He was going to knock but the door slid open, so the trio heads inside with kunai on their hands as the door shuts by itself then Sakumo Hatake who was actually hiding on the sealing comes down and he has a kunai too.

"I'll take 2 boxes of Choco lucks, lower your weapons", Sakumo ordered them.

"Sakumo if I may"

"Shut your mouth Blondie", Sakumo cuts her off.

"My name is not Blondie", Ino said with a glare.

"How did you get in?"

"Dad apologies", Kakashi said to his father.

"I know Kakashi", Sakumo respond to his son.

"Then you know why I'm here", Kakashi dumbs all of the leaf headbands into the table.

Timeskip again

"It's not like I'm getting what you're saying but an imposter fire daimyo?!"

"Well how could Sakumo say it sounds crazy", Shikamaru asked Ino.

"What did they do with the real fire daimyo?"

"We fear he's dead", Ino answered.

"I don't think so you're not going to kill your best asset", Sakumo then look at the headband of Sasuke Uchiha.

"Sasuke Uchiha tell me about him", he asked them about Sasuke.

"He was my student before becoming a great leader", Kakashi said to his father.

"He saved my life", Shikamaru said.

"Dad you think you can get close to the fire daimyo?"

"Negative Kakashi", Sakumo said to him.

**Ok this chapter is finished. Sakumo Hatake the father of Kakashi has the role of General Colton thanks to the first review. I know Sakumo status is decease long before the start of the Naruto series but since Kushina Uzumaki is still alive he too is still alive. Sakumo never died he just got frozen in time. Please review**

**Next: Red cobra ninja **


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